I am getting an error upon my local Galaxy startup which I suspect is causing an invalid tool runner entry in my left hand menu (my tool url is: http://localhost:8081/tool_runner/index instead of http://localhost:8081/tool_runner?tool_id=FLASHforFASTQ)
Here is the error I get:
galaxy.tools DEBUG 2012-03-28 13:48:28,658 Loading section: MyTools galaxy.tools DEBUG 2012-03-28 13:48:28,665 Loaded tool: sam_to_bam_QT 0.0.1 galaxy.tools DEBUG 2012-03-28 13:48:28,671 Loaded tool: BAMtoFASTQ 0.01 galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readleft: Unable to determine parameter type of test input 'readleft'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools.test DEBUG 2012-03-28 13:48:28,677 Error in add_param for readright: Unable to determine parameter type of test input 'readright'. Ensure that the parameter exists and that any container groups are defined first. galaxy.tools DEBUG 2012-03-28 13:48:28,678 Loaded tool: FLASHFASTQ 0.01
Here is the xml for my tool:
<tool id="FLASHFASTQ" name="FLASH Overlap for FASTQ" version="0.01"> <description>Finds overlaps between paired fastq files or fills the insert with N's</description> <command interpreter="python"> FLASHforFASTQ.py --readleft=$readleft --readright=$readright --output=$output1 </command> <inputs> <data format="fastqsanger" name="readleft" type="data" label="Left fastq reads FASTQ files" ftype="fastqsanger" /> <data format="fastqsanger" name="readright" type="data" label="Right fastq reads FASTQ files" ftype="fastqsanger" /> </inputs> <outputs> <param format="fasta" name="output1" type="data" label="Overlap sequences in FASTA format"/> </outputs> <tests> <test> <!-- FLASH to FASTQ conversion command: /bioinformatics/asm/bio_bin/Galaxy/galaxy-dist/tools/mytools/FLASHforFASTQ.py -lr -rr -output1 --> <param name="readleft" value="quick-taxa.r1.fastq" type="data" ftype="fastqsanger" /> <param name="readright" value="quick-taxa.r2.fastq" type="data" ftype="fastqsanger" /> <output name="output1" file="quick-taxa.fasta" ftype="fasta" /> </test> </tests> <help> **What it does**
This tool uses a modifed version of the FLASH overlapper to overlap paired end reads together and outputs the the resulting sequence in FASTA format </help> </tool>
What's the problem?!?!
Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 DBrami@SyntheticGenomics.commailto:DBrami@SyntheticGenomics.com www.SyntheticGenomics.comhttp://www.syntheticgenomics.com/